def draw(self, title=None):
fig = plt.figure()
ax = plt.gca()
A = self.to_adjacency_matrix()
scipy_dendrogram(A, color_threshold=0.7 * max(A[:, 2]))
ax.spines["bottom"].set_visible(False)
ax.spines["top"].set_visible(False)
ax.spines["left"].set_visible(False)
ax.spines["right"].set_visible(False)
fig.suptitle(title, fontsize=12)
plt.show()
def draw(self,
show=True,
save=False,
format="pdf",
labels=None,
title=None,
fontsize=None):
"""Draw the dendrogram using pylab and matplotlib."""
try:
from scipy.cluster.hierarchy import dendrogram as scipy_dendrogram
except ImportError:
raise ImportError("Scipy not installed, can't draw dendrogram")
try:
import pylab
except ImportError:
raise ImportError("Pylab not installed, can't draw dendrogram")
fig = pylab.figure()
m = self.to_linkage_matrix()
# default labels are the cluster id's (these must be matched!!)
d = scipy_dendrogram(m,
labels=labels,
leaf_font_size=fontsize,
color_threshold=0.6 * max(m[:, 2]))
if title is not None:
fig.suptitle(title, fontsize=12)
if show:
fig.show()
if save:
fig.savefig('dendrogram.%s' % (format, ))
def draw(self,
show=True,
save=False,
format="pdf",
labels=None,
title=None,
fontsize=None):
"""Draw the dendrogram using pylab and matplotlib."""
try:
from scipy.cluster.hierarchy import dendrogram as scipy_dendrogram
except ImportError:
raise ImportError("Scipy not installed, can't draw dendrogram")
try:
import pylab
except ImportError:
raise ImportError("Pylab not installed, can't draw dendrogram")
fig = pylab.figure()
m = numpy.array(self._items[0].adjacency_list(), numpy.dtype('d'))
m.view('d,d,d,d').sort(order=['f2'], axis=0)
# default labels are the cluster id's (these must be matched!!)
d = scipy_dendrogram(m,
labels=labels,
leaf_font_size=fontsize,
color_threshold=0.6 * max(m[:, 2]))
if title is not None:
fig.suptitle(title, fontsize=12)
if show:
fig.show()
if save:
fig.savefig('dendrogram.%s' % (format, ))
def dendrogram(path_to_submissions_directory, clustermap):
output_path = os.path.join(path_to_submissions_directory, 'output')
linkage_matrix = np.load(os.path.join(output_path, LINKAGE_NAME))
edit_distances = np.load(os.path.join(output_path, EDITDISTANCE_NAME))
plt.figure()
if not clustermap:
scipy_dendrogram(linkage_matrix)
else:
sns.set(font_scale=1.8)
sns.clustermap(edit_distances,
row_linkage=linkage_matrix,
col_linkage=linkage_matrix,
annot_kws={"size": 16},
cmap='YlGnBu')
output_chart_path = os.path.join(output_path, 'dendrogram.png')
plt.savefig(output_chart_path)
click.echo(f'Saved as \'{output_chart_path}\'.')
def draw_scipy_tree(self,
corpus,
fontsize=5,
color_leafs=True,
outputfile=None,
save=False,
show=True,
return_svg=True):
"""
Draw the dendrogram using plain pylab/scipy/matplotlib.
"""
plt.clf()
if outputfile:
outputfile = os.path.expanduser(outputfile)
fig = plt.figure()
ax = fig.add_subplot(111, facecolor='white')
plt.rcParams['font.family'] = 'arial'
plt.rcParams['font.size'] = 6
plt.rcParams['lines.linewidth'] = 0.75
m = self.to_linkage_matrix()
labels = corpus.titles
d = scipy_dendrogram(m,
labels=labels,
leaf_font_size=fontsize,
color_threshold=0.7 * max(m[:, 2]),
leaf_rotation=180)
ax = plt.gca()
for idx, label in enumerate(ax.get_xticklabels()):
label.set_rotation('vertical')
label.set_fontname('Arial')
label.set_fontsize(fontsize)
if color_leafs:
label.set_color(
plt.cm.get_cmap('nipy_spectral')(corpus.target_ints[idx] /
10.))
ax.get_yaxis().set_ticks([])
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.xaxis.set_ticks_position('bottom')
plt.xticks(rotation=90)
plt.tick_params(axis='x', which='both', bottom='off', top='off')
plt.tick_params(axis='y', which='both', bottom='off', top='off')
ax.xaxis.grid(False)
ax.yaxis.grid(False)
plt.rcParams["figure.facecolor"] = "white"
plt.rcParams["axes.facecolor"] = "white"
plt.rcParams["savefig.facecolor"] = "white"
plt.subplots_adjust(bottom=0.15)
if save:
fig.savefig(outputfile)
if show:
plt.show()
if return_svg:
return plt_fig_to_svg(fig)
def draw(self, show=True, save=False, format="pdf", labels=None, title=None, fontsize=None):
"""Draw the dendrogram using pylab and matplotlib."""
try:
from scipy.cluster.hierarchy import dendrogram as scipy_dendrogram
except ImportError:
raise ImportError("Scipy not installed, can't draw dendrogram")
try:
import pylab
except ImportError:
raise ImportError("Pylab not installed, can't draw dendrogram")
try:
import matplotlib.pyplot as plt
except ImportError:
raise ImportError("Matplotlib not installed, can't draw dendrogram")
fig = plt.figure()
ax = fig.add_subplot(111, axisbg='white')
plt.rcParams['font.family'] = 'arial'
plt.rcParams['font.size'] = 6
plt.rcParams['lines.linewidth'] = 0.75
m = self.to_linkage_matrix()
d = scipy_dendrogram(m, labels=labels,
leaf_font_size=fontsize,
color_threshold=0.7*max(m[:,2]),
leaf_rotation=180)
ax = plt.gca()
ax_labels = ax.get_xmajorticklabels()+ax.get_ymajorticklabels()
for i in range(len(ax_labels)):
ax_labels[i].set_family('arial')
ax.get_yaxis().set_ticks([])
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.xaxis.set_ticks_position('bottom')
plt.xticks(rotation=90)
plt.tick_params(axis='x', which='both', bottom='off', top='off')
plt.tick_params(axis='y', which='both', bottom='off', top='off')
ax.xaxis.grid(False)
ax.yaxis.grid(False)
plt.rcParams["figure.facecolor"] = "white"
plt.rcParams["axes.facecolor"] = "white"
plt.rcParams["savefig.facecolor"] = "white"
if title is not None:
fig.suptitle(title, fontsize=12)
if show:
fig.show()
if save:
fig.savefig('dendrogram.%s' % (format,))
def draw_scipy_tree(self, corpus, fontsize=5, color_leafs=True,
outputfile=None, save=False, show=True, return_svg=True):
"""
Draw the dendrogram using plain pylab/scipy/matplotlib.
"""
plt.clf()
if outputfile:
outputfile = os.path.expanduser(outputfile)
fig = sns.plt.figure()
ax = fig.add_subplot(111, axisbg='white')
plt.rcParams['font.family'] = 'arial'
plt.rcParams['font.size'] = 6
plt.rcParams['lines.linewidth'] = 0.75
m = self.to_linkage_matrix()
labels = corpus.titles
d = scipy_dendrogram(m, labels=labels,
leaf_font_size=fontsize,
color_threshold=0.7*max(m[:,2]),
leaf_rotation=180)
ax = sns.plt.gca()
for idx, label in enumerate(ax.get_xticklabels()):
label.set_rotation('vertical')
label.set_fontname('Arial')
label.set_fontsize(fontsize)
if color_leafs:
label.set_color(plt.cm.spectral(corpus.target_ints[idx] / 10.))
ax.get_yaxis().set_ticks([])
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.xaxis.set_ticks_position('bottom')
sns.plt.xticks(rotation=90)
sns.plt.tick_params(axis='x', which='both', bottom='off', top='off')
sns.plt.tick_params(axis='y', which='both', bottom='off', top='off')
ax.xaxis.grid(False)
ax.yaxis.grid(False)
sns.plt.rcParams["figure.facecolor"] = "white"
sns.plt.rcParams["axes.facecolor"] = "white"
sns.plt.rcParams["savefig.facecolor"] = "white"
sns.plt.subplots_adjust(bottom=0.15)
if save:
fig.savefig(outputfile)
if show:
sns.plt.show()
if return_svg:
return plt_fig_to_svg(fig)
def draw(self, show=True, save=False, format="pdf", labels=None, title=None, fontsize=None):
"""Draw the dendrogram using pylab and matplotlib."""
try:
from scipy.cluster.hierarchy import dendrogram as scipy_dendrogram
except ImportError:
raise ImportError("Scipy not installed, can't draw dendrogram")
try:
import pylab
except ImportError:
raise ImportError("Pylab not installed, can't draw dendrogram")
fig = pylab.figure()
m = self.to_linkage_matrix()
# default labels are the cluster id's (these must be matched!!)
d = scipy_dendrogram(m, labels=labels, leaf_font_size=fontsize,
color_threshold=0.6*max(m[:,2]))
if title is not None:
fig.suptitle(title, fontsize=12)
if show:
fig.show()
if save:
fig.savefig('dendrogram.%s' % (format,))
def draw(self,
show=True,
save=False,
format="pdf",
labels=None,
title=None,
fontsize=None):
"""Draw the dendrogram using pylab and matplotlib."""
try:
from scipy.cluster.hierarchy import dendrogram as scipy_dendrogram
except ImportError:
raise ImportError("Scipy not installed, can't draw dendrogram")
try:
import pylab
except ImportError:
raise ImportError("Pylab not installed, can't draw dendrogram")
try:
import matplotlib.pyplot as plt
except ImportError:
raise ImportError(
"Matplotlib not installed, can't draw dendrogram")
fig = plt.figure()
ax = fig.add_subplot(111, axisbg='white')
plt.rcParams['font.family'] = 'arial'
plt.rcParams['font.size'] = 6
plt.rcParams['lines.linewidth'] = 0.75
m = self.to_linkage_matrix()
d = scipy_dendrogram(m,
labels=labels,
leaf_font_size=fontsize,
color_threshold=0.7 * max(m[:, 2]),
leaf_rotation=180)
ax = plt.gca()
ax_labels = ax.get_xmajorticklabels() + ax.get_ymajorticklabels()
for i in range(len(ax_labels)):
ax_labels[i].set_family('arial')
ax.get_yaxis().set_ticks([])
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.xaxis.set_ticks_position('bottom')
plt.xticks(rotation=90)
plt.tick_params(axis='x', which='both', bottom='off', top='off')
plt.tick_params(axis='y', which='both', bottom='off', top='off')
ax.xaxis.grid(False)
ax.yaxis.grid(False)
plt.rcParams["figure.facecolor"] = "white"
plt.rcParams["axes.facecolor"] = "white"
plt.rcParams["savefig.facecolor"] = "white"
if title is not None:
fig.suptitle(title, fontsize=12)
if show:
fig.show()
if save:
fig.savefig('dendrogram.%s' % (format, ))
